documentation:vocabulary:atc
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documentation:vocabulary:atc [2016/06/13 02:14] cgreich created |
documentation:vocabulary:atc [2021/10/06 15:54] (current) ptalapova [Sources] |
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| - | ^ATC|ATC 1st|Anatomical main group|||||||| | + | ===== ATC ===== |
| - | ^:::|ATC 2nd|Therapeutic subgroup|||||||| | + | |
| - | ^:::|ATC 3rd|Pharmacological subgroup|||||||| | + | |
| - | ^:::|ATC 4th|Therapeutic/pharmacological/chemical subgroup|||||||| | + | |
| - | ^:::|ATC 5th|Chemical substance subgroup (ingredients or combinations)|||||||| | + | |
| + | The Anatomical Therapeutic Chemical (ATC) Classification System is a drug classification system that classifies the active ingredients of drugs according to the organ or system on which they act and their therapeutic, pharmacological, and chemical properties. It is controlled by the World Health Organization Collaborating Centre for Drug Statistics Methodology (WHOCC). Inasmuch as the ATC codes are semantic identifiers, the ATC vocabulary was taken as a basis for the [[https://www.ohdsi.org/2019-us-symposium-showcase-20|OMOP Drug Hierarchy]]. As of 30 September 2021, there are 6497 valid codes in the ATC. | ||
| + | |||
| + | ==== Sources ===== | ||
| + | ATC source codes are obtained from [[https://www.whocc.no/atc_ddd_index|WHOCC ATC/DDD Index 2021]] and, in OMOP, stored in the table of [[https://drive.google.com/file/d/1VX2HRw71Wac7BIN_gh5EOUxNwAF-DqwW/view?usp=sharing|class_drugs_scraper]] | ||
| + | |||
| + | ==== Transformation ===== | ||
| + | The translation of source ATC codes to the OMOP Vocabulary is presented [[https://github.com/OHDSI/Vocabulary-v5.0/tree/master/ATC|on the OHDSI GitHub]]. | ||
| + | |||
| + | ==== Concept Names ==== | ||
| + | - ATC codes of 1st-3th Classes are written in UPPERCASE. | ||
| + | - ATC codes of 4th Class are written in Initcap. | ||
| + | - ATC codes of 5th Class are written in lowercase and contain the information about Active Ingredient(s) or Ingredient Group(s) together with the route of administration. The latter is separated from the Ingredient-related information by semicolon “;”. Different routes of one Drug Product are separated by a comma “,”. | ||
| + | - OMOPized names of ATC Classes, containing information about the route of administration, are assigned by the vocabulary team through the [[https://drive.google.com/file/d/1z1SdeGG80NX_QkziS7Rs8mjnMncDIpwn/view?usp=sharing|concept_manual]] table. Details of ATC Adm.R-to-OMOP conversion are described below. | ||
| + | - Some 5th ATC Classes, which have name duplicates in other hierarchical axes, can get additional characteristics inherited from the higher ATC Class in brackets. Note, that brackets given by the source are placed before the semicolon, while OMOP-made brackets go after it. | ||
| + | - Row ATC names as well as ATC names concatenated with DDD information are stored in class_drugs_scraper and concept_synonym_manual. | ||
| + | - Either updated or deprecated ATC codes are marked with '[U]' or '[D]' at the beginning of the //concept_name// respectively. | ||
| + | |||
| + | ==== Concept Codes ==== | ||
| + | ATC codes are alphanumeriс entities of different length, which reflects their Class: | ||
| + | ^ ATC Class ^ Length ^ Code example ^ | ||
| + | | 1st | 1 character | A | | ||
| + | | 2nd | 3 characters | A01 | | ||
| + | | 3rd | 4 characters | A01A | | ||
| + | | 4th | 5 characters | A01AA | | ||
| + | | 5th | 7 characters | A01AA01 | | ||
| + | |||
| + | ==== Domains ==== | ||
| + | All [[https://athena.ohdsi.org/search-terms/terms?vocabulary=ATC&domain=Drug&standardConcept=Classification&page=1&pageSize=15&query=|ATC codes]] are of the Drug domain, however, they may be hierarchically connected to the Device or Observation (concept_class_id = ‘Substance’) domains. | ||
| + | |||
| + | ==== Concept Classes ==== | ||
| + | ^ concept_class_id ^ description ^ count ^ | ||
| + | | ATC 5th | Chemical substance subgroup (ingredients or combinations) | 5131 | | ||
| + | | ATC 4th | Therapeutic/pharmacological/chemical subgroup | 890 | | ||
| + | | ATC 3rd | Pharmacological subgroup | 267 | | ||
| + | | ATC 2nd | Therapeutic subgroup | 94 | | ||
| + | |||
| + | ==== Concept Status (Standardness) ==== | ||
| + | Valid ATC codes are Classifications, invalid ATC codes are Non-standard ones. | ||
| + | |||
| + | ==== Deprecation ==== | ||
| + | The source usually supplies replacement ATC codes for those which have been deprecated. However, there are several ATC Classes without replacement (they seem to be semantically wrong or being erroneously placed into the ATC hierarchy). | ||
| + | |||
| + | |||
| + | |||
| + | ==== Relationships ==== | ||
| + | Relationships are defined //within// ATC and //between// ATC and RxNorm, RxNorm Extension, Multilex, SNOMED, NDFRT, and VA Class. | ||
| + | |||
| + | === ATC-specific relationships (internal) ==== | ||
| + | |||
| + | ^ relationship_id ^ reverse ^ target\\ vocabulary_id ^ description ^ | ||
| + | | ATC - RxNorm | RxNorm - ATC | RxNorm, RxNorm Extension | ■ connects ATC Classes and Drug Products, but not Ingredients\\ ■ technically non-hierarchical, however, semantically it resembles the 'Subsumes' relationship_id with the reverse of 'Is a' | | ||
| + | | ATC - RxNorm pr lat | RxNorm - ATC pr lat | RxNorm, RxNorm Extension | ■ //ATC - RxNorm primary lateral// connects:\\ -- Monocomponent ATC Classes with their full semantic equivalents in the form of main active Standard Ingredients\\ -- the 1st Active Ingredient of Multicomponent ATC Classes with Standard Ingredients\\ ■ used as a Primary unambiguous link for ATC Classes with a clear and well-defined Ingredient \\ ■ non-hierarchical \\ ■ semantically, it is an equivalent to ‘Maps to’ relationship_id, and usually (except for exemptions) has such a pair in concept_relationship | | ||
| + | | ATC - RxNorm sec lat | RxNorm - ATC sec lat | RxNorm, RxNorm Extension | ■ //ATC - RxNorm secondary lateral// connects the 2nd Active Ingredient OR any subsequent Active Ingredient of a Multicomponent ATC Class to Rx/RxN Standard Ingredient\\ ■ non-hierarchical\\ ■ used as a Secondary unambiguous link for ATC Classes with clear and well-defined Ingredient(s)\\ ■ the presence of this link is a prerequisite for creating a ‘Maps to’ relationship_id | | ||
| + | | ATC - RxNorm pr up | RxNorm - ATC pr up | RxNorm, RxNorm Extension | ■ //ATC - RxNorm primary upward// connects the 1st Ingredient Groups of Multicomponent ATC Classes to respective Rx/RxN Standard Ingredients\\ ■ applied to Multicomponent ATC Classes, which names:\\ -- starts either from the Ingredient Group or the word of combinations\\ -- contains only one Ingredient Group, which is mentioned somewhere in the middle\\ ■ hierarchical (applied at the post-processing, gives +1 level of separation)\\ ■ used as Primary ambiguous link, in which ATC Class is represented with a particular group of Ingredients with a common trait\\ ■ can be used for a well-defined but diverse group of ingredients (e.g. diastase, tree pollen, feather) | | ||
| + | | ATC - RxNorm sec up | RxNorm - ATC sec up | RxNorm, RxNorm Extension | ■ //ATC - RxNorm secondary upward// connects the 2nd Ingredient Group OR any subsequent Ingredient Group OR NOT mentioned and unspecified list of Ingredients, which can be in combination with Primary lateral or Primary upward ATC Classes, to respective Rx/RxN Ingredients\\ ■ hierarchical (applied at the post-processing, gives +1 level of separation)\\ ■ refers to the Secondary ambiguous link for Multicomponent ATC Classes | | ||
| + | === Possible combinations of ATC-specific relationships used at the Ingredient level === | ||
| + | |||
| + | - ATC - RxNorm pr lat + ATC - RxNorm sec lat | ||
| + | - ATC - RxNorm pr lat + ATC - RxNorm sec up | ||
| + | - ATC - RxNorm pr up + ATC - RxNorm sec up | ||
| + | - ATC - RxNorm pr up + ATC - RxNorm sec lat | ||
| + | ==== Hierarchy ==== | ||
| + | The ATC vocabulary is the hierarchical terminology, in which "the lowest" 5th ATC Drug Classes, reflecting real Drug Products, are connected to "higher" ATC Classes (from the 4th to 1st) via the //one-step// ancestry. In OMOP, the original ATC hierarchy is extended by Standard Drug Products of RxNorm and RxNorm Extension vocabularies, which are assigned to be descendants of the 5th ATC Classes. | ||
| + | |||
| + | ==== The OMOP conversion of ATC Administration Routes ==== | ||
| + | ^ atc.adm_r ^ omop.adm_r ^ | ||
| + | | implant | implant | | ||
| + | | Inhal | inhalant | | ||
| + | | Inhal. powder | ::: | | ||
| + | | Inhal.aerosol | ::: | | ||
| + | | Inhal.powder | ::: | | ||
| + | | Inhal.solution | ::: | | ||
| + | | Instill.sol. | instillation solution | | ||
| + | | intravesical | intravesical | | ||
| + | | N | nasal | | ||
| + | | O | local oral* | | ||
| + | | O | oral | | ||
| + | | O, P | systemic | | ||
| + | | Opht | ophthalmic | | ||
| + | | oral aerosol | local oral | | ||
| + | | P | parenteral | | ||
| + | | R | rectal | | ||
| + | | s.c. implant | implant | | ||
| + | | SL | sublingual | | ||
| + | | T | topical | | ||
| + | | TD patch | transdermal | | ||
| + | | V | vaginal | | ||
documentation/vocabulary/atc.1465784089.txt.gz · Last modified: 2016/06/13 02:14 by cgreich
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